Expression diversity and evolutionary dynamics of rice duplicate genes

Yim, Won Cheol; Lee, Byung-Moo; Jang, Cheol Seong

doi:10.1007/s00438-009-0425-y

Cited by 40 publications

(37 citation statements)

References 32 publications

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“…A total of 39 genes, which exhibited one or more other genes harboring r values C 0.545 (a \ 0.01), from 61 genes included in cluster 1,562 were manually retrieved (Yim et al 2009). The gene network was visualized using the Cytoscape program (Shannon et al 2003); the expression correlations of each of the gene pairs were mapped to the node colors, numbers of genes harboring r values C 0.545 to individual gene to edge sizes and the average expression correlation of each individual gene to other genes (r values C 0.545) to edge color, respectively.…”

Section: Construction Of Co-expressed Gene Networkmentioning

confidence: 99%

“…Several lines of evidence have shown high levels of expression divergence between members of each gene family, thus suggesting the establishment of novel gene functions for gene retention (Sémon and Wolfe 2007). For example, Yim et al (2009) previously reported that more than 30% of the rice gene families evidenced a similar high degree of expression diversity between members, as compared to that of randomly selected gene pairs.…”

Section: Introductionmentioning

confidence: 96%

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A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes

et al. 2009

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The proteins harboring RING finger motif(s) have been shown to mediate protein-protein interactions that are relevant to a variety of cellular processes. In an effort to elucidate the evolutionary dynamics of the rice RING finger protein family, we have attempted to determine their genomic locations, expression diversity, and co-expressed genes via in silico analysis and semi-quantitative RT-PCR. A total of 425 retrieved genes appear to be distributed over all 12 of the chromosomes of rice with different distributions, and are reflective of the evolutionary dynamics of the rice genome. A genome-wide dataset harboring 155 gene expression omnibus sample plates evidenced some degree of differential evolutionary fates between members of RING-H2 and RING-HC types. Additionally, responses to abiotic stresses, such as salinity and drought, demonstrated that some degree of expression diversity existed between members of the RING finger protein genes. Interestingly, we determined that one RING-H2 finger protein gene (Os04g51400) manifested striking differences in expression patterns in response to abiotic stresses between leaf and culm-node tissues, further revealing responses highly similar to the majority of randomly selected co-expressed genes. The gene network of genes co-expressed with Os04g51400 may suggest some role in the salt response of the gene. These findings may shed further light on the evolutionary dynamics and molecular functional diversity of these proteins in complex cellular regulations.

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Section: Construction Of Co-expressed Gene Networkmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 96%

A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes

et al. 2009

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“…For example, Yim et al (2009) previously reported that more than 57% of rice duplicate genes generated by a whole genome duplication event occurring 70 Mya evidenced expressional divergence across a given treatment. Similarly, at least 57-73% of Arabidopsis duplicate gene pairs formed by whole genome duplications exhibited Table 6 Frequencies of the homologous genes between members of clusters including the tentative orthologous pairs of LRR RLK genes of rice and Arabidopsis expressional divergence (Blanc and Wolfe 2004).…”

Section: Discussionmentioning

confidence: 97%

“…One kbp upstream sequences of duplicate genes were downloaded from the TIGR database for rice and the TAIR databases for Arabidopsis, respectively. The numbers of conserved motifs between the upstream sequences of duplicate gene pairs were evaluated in accordance with the methods used in our previous study, with the exception of a motif size of 10 (Yim et al 2009). The P values were calculated via Wilcoxon's rank-sum test with two sided P-value for a non-parametric statistical hypothesis test in order to evaluate the differences between treatments in values between divergent and non-divergent pairs.…”

Section: Methodsmentioning

confidence: 99%

“…For another example, several lines of evidence have revealed important differences in substrate specificity among members of the Arabidopsis polyamine oxidase gene family, further supporting the notion of functional diversity following gene duplication (Fincato et al 2011). Based on the genome-wide transcriptome dataset, most gene families evidenced relatively high degrees of expressional diversity between members of each gene family, thereby suggesting that gene duplication is one of the principal forces that generate functional novelty (Yim et al 2009). Additionally, there have been some previous studies in this area, which have been conducted using a large number of plant gene families such as leucine-rich repeat extension (Baumberger et al 2003), rice wall-associated kinase gene family (Zhang et al 2005), rice F-box proteins (Jain et al 2007), basic leucine zipper transcription factor family (Nikhawan et al 2008), non-specific lipid transfer proteins (Jang et al 2008), and sugar transporter gene family (Afoufa-Bastien et al 2010).…”

Section: Introductionmentioning

confidence: 92%

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Comparative analysis of evolutionary dynamics of genes encoding leucine-rich repeat receptor-like kinase between rice and Arabidopsis

2011

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The leucine-rich repeat (LRR) receptor kinase (RLK) proteins constitute a large superfamily in the plant genome, and carry out key functions in a variety of biological pathways. In an effort to determine the evolutionary fate of members of a large gene family such as plant LRR RLK proteins we conducted in silico analysis using complete genome sequencing datasets, genome-wide transcriptome databases, and bioinformatics tools. A total of 292 and 165 LRR RLK genes were retrieved from the rice and Arabidopsis genomes, respectively, formed by diverse duplication events for gene expansion. The phylogenic analyses of the LRR RLK genes suggested combinations of LRR domains and RLK domains in the ancient plant genome prior to the divergence of rice and Arabidopsis, followed by massive independent expansions during speciation. The somewhat high frequencies (50-73%) of expressional divergence of members of duplicate gene pairs formed by whole/segmental genome duplication (W/SGD) and tandem duplication (TD) events of Arabidopsis and TD events of rice support the idea of their functional diversity for gene retention. By contrast, a relatively low degree (at least 20%) of members of rice LRR RLK gene pairs formed by W/SGD appear to be divergent in expression following the duplication event. At least 7 pairs of co-expressed gene clusters, including each of the tentative orthologous LRR RLK genes between rice and Arabidopsis, were enriched to an orthologous set between members of each of the pairs as compared to those of the random pairs, suggesting some degree of functional conservation of individual genes. These results may shed some light on the crucial functions of the plant LRR RLK genes with regard to a variety of biological processes.

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Molecular sequence variations of the lipoxygenase-2 gene in soybean

et al. 2011

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Soybean lipoxygenase genes comprise a multi-gene family, with the seed lipoxygenase isozymes LOX1, LOX2, and LOX3 present in soybean seeds. Among these, the LOX2 isozyme is primarily responsible for the "beany" flavor of most soybean seeds. The variety, Jinpumkong 2, having null alleles (lx1, lx2, and lx3) lacks the three seed lipoxygenases; so, sequence variations between the lipoxygenase-2 genes of Pureunkong (Lx2) and Jinpumkong 2 (lx2) cultivars were examined. One indel, four single nucleotide polymorphisms (SNPs), a 175-bp fragment in the 5'-flanking sequence, and a missense mutation within the coding region were found in Jinpumkong 2. The distribution of the sequence variations was investigated among 90 recombinant inbred lines (RILs) derived from a cross of Pureunkong × Jinpumkong 2 and in 480 germplasm accessions with various origins and maturity groups. Evidence for a genetic bottleneck was observed: the 175-bp fragment was rare in Glycine max, but present in the majority of the G. soja accessions. Furthermore, the 175-bp fragment was not detected in the 5' upstream region of the Lx2 gene on chromosome (Chr) 13 in Williams 82; instead, a similar 175-bp fragment was positioned in the homeologous region on Chr 15. The findings indicated that the novel fragment identified was originally present in the Lx2 region prior to the recent genome duplication in soybean, but became rare in the G. max gene pool. The missense mutation of the conserved histidine residue of the lx2 allele was developed into a single nucleotide-amplified polymorphism (SNAP) marker. The missense mutation showed a perfect correlation with the LOX2-lacking phenotype, so the SNAP marker is expected to facilitate breeding of soybean cultivars which lack the LOX2 isozyme.

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Expression diversity and evolutionary dynamics of rice duplicate genes

Cited by 40 publications

References 32 publications

A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes

A gene family encoding RING finger proteins in rice: their expansion, expression diversity, and co-expressed genes

Comparative analysis of evolutionary dynamics of genes encoding leucine-rich repeat receptor-like kinase between rice and Arabidopsis

Molecular sequence variations of the lipoxygenase-2 gene in soybean

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